Currently, there is no generic stain for the slime matrix and it often goes undetected. 1) biofilms are important in medical and dental infections, as well as industrial biofouling, 2) the EPS matrix is a hallmark characteristic of microbial biofilms and 3) the control and killing of biofilm bacteria requires different strategies than those planktonic (or single) cells. Microscopic detection of biofilm on, or associated with, surfaces is useful for basic research and has application in clinical diagnostics.
Current technologies for staining the biofilm EPS matrix are indicated in Table 1.
TABLE 1ReagentTargetLimitationLectinsStains specific sugarThere are 100s of lectins and different types ofresidues in the matrix.sugars in biofilm slime, therefore whether anyparticular one may work is hit or miss.CalcuflourUnknown - is used toGood for only a few types of biofilm.stain the cell wall offungi.Pico Green andNucleic acid in theNucleic acids are often a small component ofother nucleic acidmatrixthe slime matrix. Also since bacteriastainsthemselves stain with these stains, thebrightness tends to dim out the signal fromstain in the slime.Ruthenium redAcidic polysaccharidesGood for a very specialized microscopy calledsuch as alginate“transmission electron microscopy”.Alcian BluePolysaccharidesIncompatible with fluorescent stains since itcauses them to loose fluorescence(quenching).Crystal violetGeneral stainIncompatible with fluorescent stains since itcauses them to loose fluorescence. The vastmajority of biofilm research microscopymethods rely on visualizing bacteria withfluorescent stains.Methylene blueGeneral stainAs above